MERFISH Report

1. Overview

  • Principle Investigator: Mehrdad Shamloo

  • Institution: Stanford

  • Project: SPR22-003 Aged Sleep Deprivation study

1.1 Slice Submission

This is the detailed slice information we got from collaborators:

Sample ID Anatomical source Preparation method Treatments Species & Genetic background Sex Age
1 brain hemisphere perfused and flash frozen in OCT embedding media No Sleep Deprivation- 18 months mouse c57bl6 m 18 mo
2 brain hemisphere perfused and flash frozen in OCT embedding media No Sleep Deprivation- 18 months mouse c57bl7 m 18 mo
3 brain hemisphere perfused and flash frozen in OCT embedding media No Sleep Deprivation- 18 months mouse c57bl8 m 18 mo
23 brain hemisphere perfused and flash frozen in OCT embedding media Sleep Deprivation- 18 months mouse c57bl9 m 18 mo
24 brain hemisphere perfused and flash frozen in OCT embedding media Sleep Deprivation- 18 months mouse c57bl10 m 18 mo
25 brain hemisphere perfused and flash frozen in OCT embedding media Sleep Deprivation- 18 months mouse c57bl11 m 18 mo
31 brain hemisphere perfused and flash frozen in OCT embedding media No Sleep Deprivation- 4 months mouse c57bl12 m 4 mo
32 brain hemisphere perfused and flash frozen in OCT embedding media No Sleep Deprivation- 4 months mouse c57bl13 m 4 mo
33 brain hemisphere perfused and flash frozen in OCT embedding media No Sleep Deprivation- 4 months mouse c57bl14 m 4 mo
34 brain hemisphere perfused and flash frozen in OCT embedding media No Sleep Deprivation- 4 months mouse c57bl15 m 4 mo
35 brain hemisphere perfused and flash frozen in OCT embedding media No Sleep Deprivation- 4 months mouse c57bl16 m 4 mo
36 brain hemisphere perfused and flash frozen in OCT embedding media Sleep Deprivation- 4 months mouse c57bl17 m 4 mo
37 brain hemisphere perfused and flash frozen in OCT embedding media Sleep Deprivation- 4 months mouse c57bl18 m 4 mo
38 brain hemisphere perfused and flash frozen in OCT embedding media Sleep Deprivation- 4 months mouse c57bl19 m 4 mo
39 brain hemisphere perfused and flash frozen in OCT embedding media Sleep Deprivation- 4 months mouse c57bl20 m 4 mo
40 brain hemisphere perfused and flash frozen in OCT embedding media Sleep Deprivation- 4 months mouse c57bl21 m 4 mo

1.2 Sample Information

A brief sample information is generated from the submission table for the following analysis.

“SD” refers to “Sleep Deprivation” while “nSD” refers to “No Sleep Deprivation”.

Sample Index and Basic Information
Batch Index Genotype region Mice Age (month) Data Path
1 nSD1 nSD region_0 18 202310191044_20231019StanfordSD1n23VZG191m500x01_VMSC00101
1 SD23 SD region_1 18 202310191044_20231019StanfordSD1n23VZG191m500x01_VMSC00101
2 nSD2 nSD region_0 18 202311201155_20231120StanfordSD2n24VZG191m500x02_VMSC05201
2 SD24 SD region_1 18 202311201155_20231120StanfordSD2n24VZG191m500x02_VMSC05201
3 nSD3 nSD region_0 18 202312121344_20231212StanfordSD3n25VZG191x500x01_VMSC05201
3 SD25 SD region_1 18 202312121344_20231212StanfordSD3n25VZG191x500x01_VMSC05201
4 SD36 SD region_0 4 202312151433_20231215StanfordSD3136VZG191m500x4mx01_VMSC00101
4 nSD31 nSD region_1 4 202312151433_20231215StanfordSD3136VZG191m500x4mx01_VMSC00101
5 SD37 SD region_0 4 202312271640_20231227StanfordSD4m3237VZG191x500x02_VMSC00101
5 nSD32 nSD region_1 4 202312271640_20231227StanfordSD4m3237VZG191x500x02_VMSC00101
6 SD38 SD region_0 4 202312271749_20231227Stanford4mSD3338VZG191x500x3_VMSC05201
6 nSD33 nSD region_1 4 202312271749_20231227Stanford4mSD3338VZG191x500x3_VMSC05201

1.3 MERSCOPE Data Quality Summary

The summaries present the data quality assessment automatically generated by MERSCOPE for each experiment. We mainly focus on the transcripts level for each sample. So we’re looking for high density in transcripts, based on the transcripts count per field of view (FOV), transcript density in FOV, and frequency of transcripts detected.

Generally, log10 transcript count > 5.0 in most area can be considered as a good quality standard.

Need to note that the low accuracy in DAPI cell boundary is not a concern, as a self-designed cell segmentation processing will take over this task.

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

2. Data Processing & Analysis

2.1 Cell Segmentation

Based on the spatial information and images obtained from MERFISH, we developed a machine learning model using the Cellpose algorithm to distinguish individual cells via MERFISH DAPI images.

To ensure the data quality and accuracy of cells, we have defined the minimum and maximum values for cell volume and gene count per cell. The cell volume should be between [100, 1800], and the gene count per cell > 25. After filter the outliers, the qualified cells count is shown in the following table.

Outliers were filtered from the data, and the qualified cells count is presented in the following table. The identified cells after filtering are listed in the following table. In total, the study identified ** 712944** cells across 12 samples.

Segmented Cell Count in each Samples
Sample Index Cell Count
SD36 66786
SD24 65480
nSD31 62351
SD25 60474
SD23 59687
nSD3 58384
nSD2 57578
SD37 57423
nSD32 56953
nSD1 56686
nSD33 56259
SD38 54883
Identified Cell Spatial Overview on all Samples

Identified Cell Spatial Overview on all Samples

2.2 Batch Effect & Dimension Reduction

We use Scanpy for the analysis of single-cell level transcriptome data. The initial stage of our analysis involves the elimination of batch effects, thereby ensuring that different samples from various batches are distributed within the same domain and are statistically reasonable to be integrated and compared. To achieve this, we utilize the Harmony algorithm.

Subsequently, we present visualizations of the batch difference by Leiden UMAP clusters. Also, we illustrate the distributions of the Leiden clusters for future analysis.

Transcript counts on each sample

Transcript counts on each sample

Umap of cells and colored by batch

Umap of cells and colored by batch

Umap of cells on each batch

Umap of cells on each batch

Leiden Umap can be dividied to 28 clusters

Leiden Umap can be dividied to 28 clusters

2.3 Cell Annotation

We use a recent published tool: Map My Cell to perform cell type annotations for each cell. It is a high resolution cell type annotator build by Alan Institude, with nested levels of classification including 34 classes and 338 subclasses.

The taxonomy is based on the Allen Mouse Brain Common Coordinate Framework version 3 (CCFv3)[https://doi.org/10.1016/j.cell.2020.04.007]. Part of the used abbreviations is list in the supplementary Abbreviation. Otherwise can be found in CCFv3 paper.

With the annotation, we can identify and plot the selected types of cells in each sample.

2.3.1 Low Resolution Class

MapMyCell Annotation Cell Count (Low resolution class)
class_name count
31 OPC-Oligo 168524
30 Astro-Epen 112863
33 Vascular 80432
01 IT-ET Glut 79488
09 CNU-LGE GABA 46138
02 NP-CT-L6b Glut 26178
19 MB Glut 23711
20 MB GABA 23531
34 Immune 19905
12 HY GABA 17968
18 TH Glut 16273
27 MY GABA 13050
11 CNU-HYa GABA 12030
10 LSX GABA 9649
07 CTX-MGE GABA 8601
14 HY Glut 8382
23 P Glut 7868
26 P GABA 6320
24 MY Glut 5293
06 CTX-CGE GABA 5004
08 CNU-MGE GABA 4806
05 OB-IMN GABA 4294
13 CNU-HYa Glut 3073
32 OEC 2658
04 DG-IMN Glut 1602
21 MB Dopa 1572
28 CB GABA 1073
03 OB-CR Glut 624
29 CB Glut 529
17 MH-LH Glut 524
22 MB-HB Sero 516
16 HY MM Glut 373
25 Pineal Glut 57
15 HY Gnrh1 Glut 35

2.3.2 High Resolution Class

MapMyCell Annotation Cell Count (High resolution subclass)
subclass_name count
7 327 Oligo NN 155504
3 333 Endo NN 51244
11 318 Astro-NT NN 42990
0 319 Astro-TE NN 42944
183 062 STR D2 Gaba 19098
12 334 Microglia NN 17604
31 030 L6 CT CTX Glut 17454
191 061 STR D1 Gaba 16343
24 006 L4/5 IT CTX Glut 15131
8 331 Peri NN 14424
5 321 Astroependymal NN 14038
2 326 OPC NN 13020
219 151 TH Prkcd Grin2c Glut 10526
20 004 L6 IT CTX Glut 9409
17 007 L2/3 IT CTX Glut 8913
146 181 IC Tfap2d Maf Glut 8894
32 005 L5 IT CTX Glut 8516
50 010 IT AON-TT-DP Glut 8110
1 330 VLMC NN 7734
18 009 L2/3 IT PIR-ENTl Glut 6929
195 063 STR D1 Sema5a Gaba 6476
130 323 Ependymal NN 5675
9 332 SMC NN 5206
44 022 L5 ET CTX Glut 5082
60 020 L2/3 IT RSP Glut 4968
26 052 Pvalb Gaba 4876
46 285 MY Lhx1 Gly-Gaba 4508
43 016 CA1-ProS Glut 4380
59 101 ZI Pax6 Gaba 3944
54 029 L6b CTX Glut 3579
42 325 CHOR NN 3337
30 053 Sst Gaba 3146
40 069 LSX Nkx2-1 Gaba 3131
62 032 L5 NP CTX Glut 3123
78 093 RT-ZI Gnb3 Gaba 2933
10 328 OEC NN 2658
38 017 CA3 Glut 2654
204 060 OT D3 Folh1 Gaba 2452
180 235 PG-TRN-LRN Fat2 Glut 2381
69 198 IC Six3 En2 Gaba 2366
131 202 PRT Tcf7l2 Gaba 2338
33 070 LSX Prdm12 Slit2 Gaba 2262
76 098 AHN-SBPV-PVHd Pdrm12 Gaba 2229
21 046 Vip Gaba 2212
29 071 LSX Prdm12 Zeb2 Gaba 2205
107 300 PARN-MDRNd-NTS Gbx2 Gly-Gaba 2160
225 148 AV Col27a1 Glut 2025
72 320 Astro-OLF NN 1987
205 154 PF Fzd5 Glut 1971
135 207 SCs Dmbx1 Gaba 1829
4 329 ABC NN 1824
52 201 PAG-RN Nkx2-2 Otx1 Gaba 1794
141 205 SC-PAG Lef1 Emx2 Gaba 1789
53 041 OB-in Frmd7 Gaba 1778
260 129 VMH Nr5a1 Glut 1776
118 057 NDB-SI-MA-STRv Lhx8 Gaba 1753
167 243 PGRN-PARN-MDRN Hoxb5 Glut 1702
85 306 SPVI-SPVC Sall3 Lhx1 Gly-Gaba 1687
6 049 Lamp5 Gaba 1648
271 104 TU-ARH Otp Six6 Gaba 1634
273 215 SNc-VTA-RAmb Foxa1 Dopa 1572
188 037 DG Glut 1569
108 064 STR-PAL Chst9 Gaba 1415
236 134 PH-ant-LHA Otp Bsx Glut 1351
148 222 PB Evx2 Glut 1343
138 213 SCsg Gabrr2 Gaba 1340
82 304 NTS-PARN Neurod2 Gly-Gaba 1314
77 195 SNr-VTA Pax5 Npas1 Gaba 1278
34 338 Lymphoid NN 1265
73 203 LGv-SPFp-SPFm Nkx2-2 Tcf7l2 Gaba 1248
152 090 BST-MPN Six3 Nrgn Gaba 1244
13 210 PRT Mecom Gaba 1216
282 102 DMH-LHA Gsx1 Gaba 1182
28 199 PAG-MRN-RN Foxa2 Gaba 1171
105 209 SCs Pax7 Nfia Gaba 1121
222 107 DMH Hmx2 Gaba 1067
99 089 PVR Six3 Sox3 Gaba 1064
192 081 ACB-BST-FS D1 Gaba 1046
264 086 MPO-ADP Lhx8 Gaba 1042
196 088 BST Tac2 Gaba 1024
142 073 MEA-BST Sox6 Gaba 1005
143 068 LSX Otx2 Gaba 1004
215 106 PVpo-VMPO-MPN Hmx2 Gaba 996
209 182 CUN-PPN Evx2 Meis2 Glut 996
229 217 PB Lmx1a Glut 987
74 200 PAG-ND-PCG Onecut1 Gaba 981
137 187 SCsg Pde5a Glut 959
171 176 SCig Foxb1 Glut 955
93 002 IT EP-CLA Glut 926
47 045 OB-STR-CTX Inh IMN 922
23 047 Sncg Gaba 919
102 056 Sst Chodl Gaba 909
147 119 SI-MA-LPO-LHA Skor1 Glut 895
90 264 PRNc Otp Gly-Gaba 894
70 322 Tanycyte NN 893
56 251 NTS Dbh Glut 865
144 085 SI-MPO-LPO Lhx8 Gaba 864
79 317 Astro-CB NN 860
139 208 SC Lef1 Otx2 Gaba 857
217 168 SPA-SPFm-SPFp-POL-PIL-PoT Sp9 Glut 854
155 177 SCig-an-PPT Foxb1 Glut 850
88 076 MEA-BST Lhx6 Nfib Gaba 848
216 100 AHN Onecut3 Gaba 837
227 224 PCG-PRNr Vsx2 Nkx6-1 Glut 830
66 033 NP SUB Glut 826
110 054 STR Prox1 Lhx6 Gaba 825
169 180 SCiw Pitx2 Glut 824
226 164 APN C1ql4 Glut 812
124 147 AD Serpinb7 Glut 774
207 173 PAG Pou4f2 Glut 773
101 039 OB Meis2 Thsd7b Gaba 769
91 221 LDT-PCG Vsx2 Lhx4 Glut 747
133 212 SCs Lef1 Gli3 Gaba 746
116 103 PVHd-DMH Lhx6 Gaba 744
114 025 CA2-FC-IG Glut 742
81 267 CS-PRNr-PCG Tmem163 Otp Gaba 739
87 021 L4 RSP-ACA Glut 728
157 172 PAG Pou4f1 Ebf2 Glut 722
281 074 MEA-BST Lhx6 Sp9 Gaba 721
193 058 PAL-STR Gaba-Chol 721
250 132 AHN-RCH-LHA Otp Fezf1 Glut 706
194 079 CEA-BST Six3 Cyp26b1 Gaba 702
14 337 DC NN 677
182 278 NLL Gata3 Gly-Gaba 670
159 162 CUN Evx2 Lhx2 Glut 655
92 072 LSX Sall3 Lmo1 Gaba 655
49 283 PRP Otp Gly-Gaba 642
249 108 ARH-PVp Tbx3 Gaba 639
104 196 PAG-PPN Pax5 Sox21 Gaba 638
96 265 PB Sst Gly-Gaba 625
267 082 CEA-BST Ebf1 Pdyn Gaba 611
22 192 PPN-CUN-PCG Otp En1 Gaba 604
198 055 STR Lhx8 Gaba 598
83 270 LDT-DTN Gata3 Nfix Gaba 591
75 023 SUB-ProS Glut 583
165 238 NTS Phox2b Glut 574
95 027 L6b EPd Glut 568
311 128 VMH Fezf1 Glut 557
36 305 SPVI-SPVC Sall3 Nfib Gly-Gaba 551
224 163 APN C1ql2 Glut 544
223 150 CM-IAD-CL-PCN Sema5b Glut 543
181 175 SC Bnc2 Glut 538
154 169 PAG-SC Pou4f1 Zic1 Glut 531
48 003 L5/6 IT TPE-ENT Glut 520
235 216 MB-MY Tph2 Glut-Sero 516
51 277 DTN-LDT-IPN Otp Pax3 Gaba 515
201 161 PAG Pou4f3 Glut 507
27 019 L2/3 IT PPP Glut 490
203 268 CS-PRNr-DR En1 Sox2 Gaba 485
239 080 CEA-AAA-BST Six3 Sp9 Gaba 485
261 124 MPN-MPO-PVpo Hmx2 Glut 478
160 174 PAG Pou4f2 Mesi2 Glut 476
248 133 PVH-SO-PVa Otp Glut 471
240 094 SCH Six6 Cdc14a Gaba 461
149 146 LH Pou4f1 Sox1 Glut 446
120 035 OB Eomes Ms4a15 Glut 424
156 170 PAG-MRN Tfap2b Glut 418
258 311 CBX MLI Megf11 Gaba 414
125 042 OB-out Frmd7 Gaba 405
35 028 L6b/CT ENT Glut 403
128 197 SNr Six3 Gaba 402
158 171 PAG Pou4f1 Bnc2 Glut 399
202 067 LSX Sall3 Pax6 Gaba 392
136 211 SC Tnnt1 Gli3 Gaba 384
134 139 PH-LHA Foxb1 Glut 380
212 166 MRN Pou3f1 C1ql4 Glut 379
305 136 PMv-TMv Pitx2 Glut 375
161 167 PRC-PAG Tcf7l2 Irx2 Glut 375
283 135 STN-PSTN Pitx2 Glut 367
61 194 MRN-VTN-PPN Pax5 Cdh23 Gaba 363
16 263 CS-RPO Meis2 Gaba 359
173 206 SCm-PAG Cdh23 Gaba 355
151 083 CEA-BST Rai14 Pdyn Crh Gaba 354
19 018 L2 IT PPP-APr Glut 352
163 160 PAG-SC Neurod2 Meis2 Glut 351
279 111 TRS-BAC Sln Glut 344
71 299 MARN-PPY Ngfr Gly-Gaba 341
15 271 NI-RPO Gata3 Nr4a2 Gaba 338
295 117 LHA Barhl2 Glut 333
213 193 MRN-PPN-CUN Pax8 Gaba 331
132 066 NDB-SI-ant Prdm12 Gaba 326
244 110 BST-po Iigp1 Glut 320
140 246 CU-ECU-SPVI Foxb1 Glut 320
247 141 PH-SUM Foxa1 Glut 319
127 254 VCO Mafa Meis2 Glut 319
208 144 MM Foxb1 Glut 316
106 051 Pvalb chandelier Gaba 306
164 245 SPVI-SPVC Tlx3 Ebf3 Glut 306
129 087 MPN-MPO-LPO Lhx6 Zfhx3 Gaba 302
64 272 LDT-PCG-CS Gata3 Lhx1 Gaba 302
175 188 SCop Sln Glut 296
231 165 PAG-MRN Pou3f1 Glut 290
189 013 COAp Grxcr2 Glut 284
200 092 TMv-PMv Tbx3 Hist-Gaba 283
55 314 CB Granule Glut 280
179 140 PMd-LHA Foxb1 Glut 280
199 126 ARH-PVp Tbx3 Glut 276
296 097 PVHd-SBPV Six3 Prox1 Gaba 275
25 050 Lamp5 Lhx6 Gaba 273
57 229 PB-NTS Phox2b Ebf3 Lmx1b Glut 270
109 012 MEA Slc17a7 Glut 268
252 115 MS-SF Bsx Glut 264
115 335 BAM NN 258
100 315 DCO UBC Glut 249
303 125 DMH Hmx2 Glut 248
103 044 OB Dopa-Gaba 246
170 220 PB Pax5 Glut 245
302 127 DMH-LHA Vgll2 Glut 244
277 155 PRC-PAG Pax6 Glut 242
245 152 RE-Xi Nox4 Glut 238
98 313 CBX Purkinje Gaba 237
185 099 SBPV-PVa Six6 Satb2 Gaba 235
293 131 LHA-AHN-PVH Otp Trh Glut 230
232 287 MV-SPIV-PRP Dmbx1 Gly-Gaba 228
290 118 ADP-MPO Trp73 Glut 227
122 048 RHP-COA Ndnf Gaba 225
176 105 TMd-DMH Foxd2 Gaba 223
162 237 PRP-NI-PRNc-GRN Otp Glut 212
197 225 PRNc-NI-SG-RPO Vsx2 Nr4a2 Glut 209
174 279 PSV Pax2 Gly-Gaba 205
187 114 COAa-PAA-MEA Barhl2 Glut 204
119 290 MY Prox1 Lmo7 Gly-Gaba 203
126 036 HPF CR Glut 200
177 261 HB Calcb Chol 197
238 109 LGv-ZI Otx2 Gaba 197
270 231 IPN-LDT Vsx2 Nkx6-1 Glut 189
145 257 SPVC Ccdc172 Glut 188
246 156 MB-ant-ve Dmrta2 Glut 184
41 293 PAS-MV Ebf2 Gly-Gaba 184
58 308 DCO Il22 Gly-Gaba 182
113 059 GPe-SI Sox6 Cyp26b1 Gaba 181
269 248 MV-SPIV Zic4 Neurod2 Glut 179
45 065 IA Mgp Gaba 173
287 223 B-PB Nr4a2 Glut 172
84 214 IPN Otp Crisp1 Gaba 166
326 292 MV Nkx6-1 Gly-Gaba 165
298 276 LDT-PCG St18 Gaba 164
39 008 L2/3 IT ENT Glut 157
166 149 PVT-PT Ntrk1 Glut 148
67 204 SC Otx2 Gcnt4 Gaba 145
309 116 AVPV-MEPO-SFO Tbr1 Glut 140
153 303 IRN Dmbx1 Pax2 Gly-Gaba 138
172 186 SCop Pou4f2 Neurod2 Glut 136
63 273 PDTg-PCG Pax6 Gaba 130
186 228 PSV Pvalb Lhx2 Glut 130
285 294 MV Pax6 Gly-Gaba 127
168 178 SCig Foxb1 Otx2 Glut 125
297 130 LHA Pmch Glut 124
117 034 NP PPP Glut 123
86 043 OB-mi Frmd7 Gaba 118
286 282 POR Spp1 Gly-Gaba 117
265 288 MDRN Hoxb5 Ebf2 Gly-Gaba 116
254 179 SCdg-PAG Tfap2b Glut 114
278 284 GRN-IRN-MDRNd Ikzf1 Gly-Gaba 114
259 316 Bergmann NN 113
292 084 BST-SI-AAA Six3 Slc22a3 Gaba 113
230 298 PRP Gata3 Slc6a5 Gly-Gaba 112
294 121 MEA-BST Otp Zic2 Glut 111
210 309 CB PLI Gly-Gaba 110
221 113 MEA-COA-BMA Ccdc42 Glut 109
228 233 NLL-SOC Spp1 Glut 108
184 296 RPA Pax6 Hoxb5 Gly-Gaba 108
178 185 SCig Tfap2b Chrnb3 Glut 103
262 159 IF-RL-CLI-PAG Foxa1 Glut 102
68 031 CT SUB Glut 102
220 226 PRNc-PARN Tlx1 Glut 102
65 336 Monocytes NN 101
251 078 SI-MA-ACB Ebf1 Bnc2 Gaba 100
313 312 CBX MLI Cdh22 Gaba 100
214 247 MV-SPIV Phox2b Ebf3 Lbx1 Glut 99
233 234 MEV Ppp1r1c Glut 96
111 075 MEA-BST Lhx6 Nr2e1 Gaba 95
37 014 LA-BLA-BMA-PA Glut 95
256 138 PH Pitx2 Glut 95
94 011 L2 IT ENT-po Glut 93
234 286 PPY-PGRNl Vip Glyc-Gaba 90
268 077 CEA-BST Gal Avp Gaba 84
206 157 RN Spp1 Glut 82
315 145 MH Tac2 Glut 78
263 281 POR Gata3 Gly-Gaba 74
211 123 DMH Nkx2-4 Glut 73
314 297 CU-ECU Pax2 Gly-Gaba 71
266 191 PAG-MRN Rln3 Gaba 69
317 232 LDT Vsx2 Nkx6-1 Nfib Glut 68
80 001 CLA-EPd-CTX Car3 Glut 68
237 291 NTS-MDRNd Prox1 Zic1 Gly-Gaba 67
308 122 LHA-MEA Otp Glut 65
253 256 SPVC Mafa Glut 65
310 252 DMX VII Tbx20 Chol 63
190 015 ENTmv-PA-COAp Glut 61
112 302 MV Xdh Gly-Gaba 60
306 143 MM-ant Foxb1 Glut 57
243 262 Pineal Crx Glut 57
97 040 OB Trdn Gaba 56
257 158 MRN-PAG Nkx6-1 Glut 54
307 230 PRNr Otp Nfib Glut 53
150 153 MG-POL-SGN Nts Glut 48
280 091 ARH-PVi Six6 Dopa-Gaba 47
323 269 LDT Fgf7 Gaba 47
218 190 ND-INC Foxd2 Glut 45
241 275 PDTg Otp Olig3 Gaba 42
274 250 CBN Neurod2 Pvalb Glut 39
334 253 IO Fgl2 Glut 38
332 112 GPi Tbr1 Cngb3 Gaba-Glut 37
291 142 HY Gnrh1 Glut 35
242 038 DG-PIR Ex IMN 33
321 137 PH-an Pitx2 Glut 32
316 244 MV-SPIV Slc6a2 Glut 32
330 096 PVHd Gsc Gaba 31
304 310 CBX Golgi Gly-Gaba 30
319 324 Hypendymal NN 26
301 184 PAG Tcf24 Glut 26
123 307 RO-RPA Pkd2l1 Gaba 25
300 120 MEA Otp Foxp2 Glut 24
288 026 NLOT Rho Glut 23
276 255 SPVO Mafa Meis2 Glut 20
299 218 PSV Lmx1a Trpv6 Glut 19
327 239 MARN-GRN Pyy Glut 19
275 295 CBN Dmbx1 Gaba 19
329 236 IRN Vip Glut 16
272 258 SPVC Nmu Glut 13
255 289 MDRNd Prox1 Pax6 Gly-Gaba 13
324 274 PDTg Otp Shroom3 Gaba 12
322 242 PGRNd Dmbx1 Glut 12
289 095 DMH Prdm13 Gaba 11
333 266 PRNc Prox1 Brs3 Gly-Gaba 9
318 227 PB-PSV Phox2b Glut 8
312 301 MV Nr4a2 Gly-Gaba 7
284 219 PB-SUT Tlx3 Lhx2 Glut 7
331 240 MDRNv Lhx4 Qrfprl Glut 7
89 024 L5 PPP Glut 6
328 249 NTS Aldh1a2 Glut 6
325 189 PAG Ucn Glut 3
320 260 MDRNv Crp Glut 2
121 280 NLL-po Pax7 Gaba 2
335 183 PBG Mtnr1a Glut-Chol 1

2.3.3 Selected Cell Class

Selected Cell Count (Customed subclass)
select_class_name count
1 Astrocyte 96912
2 Endo 50134
9 L6b Glut 21511
5 L2/3 Glut 20604
3 Microglia 17253
10 L5 Glut 16403
19 TH Glut 15993
8 L4/5 Glut 14734
11 MY GABA 12482
7 L6 Glut 9129
14 P Glut 7729
4 P GABA 6187
18 MY Glut 5163
17 CA1 Glut 4268
12 CA3 Glut 2579
20 DG Glut 1548
16 CA2 Glut 717
15 L4 Glut 698
13 L5/6 Glut 505
6 L2 Glut 438

2.3.4 Selected Cell Type Umap

2.3.4 Selected Cell Type Spatial Map

2.3.5 Selected Cell Type Proportion

3. Manual Region Selection

Manual selection mostly based on the cell type annotation.

3.1 Hippocampus

3.2 Frontal Cortex

3.3 Locus ceruleus (Undone!)

To find LC region, we tries to show LC marker gene expression: Th, Dbh.

Dbh Gene Spatial Map

4. Gene differentiation

Here, we use pseudo-bulk and DESeq2 to compute gene differential expression. The statistical significance was cut-off by log2(FoldChange) > 1 and p_adj < 0.05.

4.2 Hippocampus Region

4.2.1 Hippocampus, 4m, SD vs nSD

##            baseMean log2FoldChange     lfcSE       stat       pvalue
## Slc6a3    1364.9733       3.426921 1.0608331   3.230405 1.236148e-03
## Adora2a   4862.6254      -3.351775 0.3519800  -9.522628 1.688538e-21
## Ppp1r1b  27366.2013      -3.300389 0.3037854 -10.864212 1.706912e-27
## Six3      2598.3987      -2.989373 0.4616998  -6.474710 9.499396e-11
## Th        3121.3955       2.903303 1.1774378   2.465780 1.367151e-02
## Penk     13809.5894      -2.737112 0.2842345  -9.629770 5.986357e-22
## Clic6     2858.5186      -2.671303 0.9943850  -2.686387 7.222931e-03
## Col6a1   15572.4225      -2.581616 0.8902951  -2.899731 3.734828e-03
## Pdyn      1785.1284      -2.578127 0.3627920  -7.106350 1.191520e-12
## Drd1      2654.5030      -2.556341 0.3079737  -8.300517 1.036590e-16
## Ccdc153   1152.1289      -2.430435 0.9757703  -2.490786 1.274609e-02
## Agt      12179.6525       1.955604 0.4041071   4.839322 1.302826e-06
## C3         823.6469      -1.847138 0.6055476  -3.050360 2.285672e-03
## Dlx2      1389.3752      -1.834641 0.3734112  -4.913193 8.960503e-07
## Nxph4     1215.3648       1.815283 0.3628801   5.002432 5.661141e-07
## Drd2      2127.2297      -1.802835 0.3928696  -4.588888 4.456129e-06
## Car12     2386.4167      -1.693730 0.4409146  -3.841401 1.223340e-04
## Syt6      5383.2729      -1.664975 0.3394866  -4.904391 9.371765e-07
## Meis2     4755.4902      -1.586100 0.3181207  -4.985844 6.169181e-07
## Syndig1l  5410.1288      -1.567867 0.3873430  -4.047750 5.171239e-05
## Tac1       791.5129      -1.537814 0.2851293  -5.393391 6.914011e-08
## Chrm4     3350.4567      -1.485698 0.3829944  -3.879164 1.048161e-04
## Folr1      534.5439      -1.427654 0.4954915  -2.881289 3.960527e-03
## Cpne5     3512.1566      -1.402412 0.3811532  -3.679391 2.337913e-04
## Dclk3    15621.4163      -1.328636 0.2701100  -4.918869 8.704560e-07
## Npas1     2269.9177       1.291786 0.3929731   3.287212 1.011847e-03
## Sncg      1409.8866       1.265045 0.2997710   4.220038 2.442607e-05
## Scn4b    10629.0169      -1.245762 0.2326462  -5.354750 8.567492e-08
## Lhx6      1508.6415      -1.214062 0.3464598  -3.504193 4.579936e-04
## Fosb      1425.5005      -1.213112 0.4931950  -2.459701 1.390528e-02
## Calb2     4308.3281       1.130460 0.3453881   3.273013 1.064075e-03
## Gpr83     1117.1038      -1.122101 0.3762036  -2.982695 2.857224e-03
## Egr4      1225.2874      -1.108319 0.4230891  -2.619588 8.803608e-03
## Fibcd1    4154.3541       1.021081 0.3070405   3.325558 8.824170e-04
##                  padj
## Slc6a3   2.060247e-02
## Adora2a  2.814230e-19
## Ppp1r1b  8.534562e-25
## Six3     7.916163e-09
## Th       1.287526e-01
## Penk     1.496589e-19
## Clic6    8.025479e-02
## Col6a1   5.187261e-02
## Pdyn     1.191520e-10
## Drd1     1.295737e-14
## Ccdc153  1.225585e-01
## Agt      4.652949e-05
## C3       3.571362e-02
## Dlx2     3.604525e-05
## Nxph4    3.084590e-05
## Drd2     1.485376e-04
## Car12    2.912714e-03
## Syt6     3.604525e-05
## Meis2    3.084590e-05
## Syndig1l 1.436455e-03
## Tac1     4.938579e-06
## Chrm4    2.620403e-03
## Folr1    5.352063e-02
## Cpne5    4.870653e-03
## Dclk3    3.604525e-05
## Npas1    1.806870e-02
## Sncg     7.184137e-04
## Scn4b    5.354682e-06
## Lhx6     8.807569e-03
## Fosb     1.287526e-01
## Calb2    1.834611e-02
## Gpr83    4.081749e-02
## Egr4     9.365540e-02
## Fibcd1   1.634106e-02

4.2.2 Hippocampus, 4m, SD vs nSD

##    baseMean log2FoldChange     lfcSE     stat      pvalue      padj
## Th 444.3555       1.218214 0.3923819 3.104665 0.001904947 0.9486635

4.2.3 Hippocampus, SD, 18m vs 4m

##           baseMean log2FoldChange     lfcSE      stat       pvalue         padj
## Th       3052.3640       3.295128 1.2070304  2.729946 6.334464e-03 0.0564445969
## Slc6a3   1410.1921       3.031186 1.0954631  2.767037 5.656841e-03 0.0532596878
## Clic6    2843.6548      -2.652370 1.0472127 -2.532790 1.131586e-02 0.0842778202
## Mapk1    1646.6096      -2.601200 0.5346434 -4.865299 1.142840e-06 0.0004100324
## Folr1     842.4595      -2.256637 0.4850865 -4.652030 3.286833e-06 0.0004100324
## Htr2c    1065.0025      -2.006609 0.4868787 -4.121375 3.766183e-05 0.0023491568
## Ppp1r1b 11668.3012      -1.847722 0.9266973 -1.993879 4.616532e-02 0.2094226917
## Coch      607.6535      -1.662861 0.4105028 -4.050791 5.104478e-05 0.0026016784
## Car12    2326.7882      -1.633785 0.4519679 -3.614824 3.005514e-04 0.0083319525
## Synpr     300.0868      -1.617818 0.4065541 -3.979343 6.910605e-05 0.0028736600
## Rims1    2134.3668      -1.607618 0.3527274 -4.557678 5.172227e-06 0.0005161883
## Pten      764.4947      -1.495198 0.4591520 -3.256435 1.128209e-03 0.0194129719
## Enpp2   18609.8516      -1.480111 0.3178592 -4.656499 3.216324e-06 0.0004100324
## Aph1b     329.6147      -1.475409 0.4198520 -3.514118 4.412171e-04 0.0104841596
## Six3     1102.9927      -1.470478 0.3484817 -4.219669 2.446609e-05 0.0017440827
## Crebbp    761.6576      -1.448981 0.4694416 -3.086606 2.024559e-03 0.0323601810
## Cdh9      698.2533      -1.438795 0.3270097 -4.399854 1.083238e-05 0.0009008925
## Drd1     1431.4307      -1.425556 0.4798458 -2.970862 2.969651e-03 0.0389962098
## Penk     6653.8594      -1.418103 0.7007292 -2.023754 4.299551e-02 0.2043310386
## Cd63      533.2938      -1.402621 0.3634884 -3.858777 1.139558e-04 0.0037000153
## Nrn1     3057.5798      -1.388018 0.2931926 -4.734153 2.199722e-06 0.0004100324
## Ccdc153   648.7175      -1.363386 0.4906130 -2.778943 5.453604e-03 0.0523336258
## Scimp     819.8027      -1.331683 0.3309819 -4.023432 5.735620e-05 0.0026018858
## Enpp6     368.9844      -1.310251 0.3238521 -4.045831 5.213784e-05 0.0026016784
## Npy1r     826.0087      -1.280637 0.3295594 -3.885906 1.019489e-04 0.0037000153
## Gm14964   673.3834      -1.252375 0.3754005 -3.336105 8.496121e-04 0.0157020901
## Gpr37    3649.2234      -1.224901 0.3515209 -3.484574 4.929207e-04 0.0106942350
## Cd2ap    1345.4934      -1.180886 0.4410368 -2.677524 7.416863e-03 0.0610002285
## Tnik      688.3765      -1.179340 0.4184830 -2.818132 4.830389e-03 0.0482072797
## Kctd4    1780.9795      -1.171516 0.3202757 -3.657837 2.543528e-04 0.0074660017
## Nectin3   674.0201      -1.162438 0.4570742 -2.543215 1.098377e-02 0.0830439518
## Gng2     1847.0245      -1.159588 0.4114552 -2.818259 4.828481e-03 0.0482072797
## Tac1      646.8013      -1.117581 0.4106281 -2.721637 6.495941e-03 0.0568679790
## Pdyn      816.2053      -1.116282 0.3284513 -3.398621 6.772652e-04 0.0140814728
## Kcnh7    1099.7148      -1.113718 0.3777099 -2.948606 3.192106e-03 0.0394160686
## Mas1     2100.2391      -1.093538 0.2841153 -3.848924 1.186378e-04 0.0037000153
## Cxcl10    235.2083       1.090587 0.3083791  3.536514 4.054450e-04 0.0101158539
## Fmo1      376.0314      -1.075141 0.3814375 -2.818656 4.822522e-03 0.0482072797
## Creb1     460.1756      -1.051940 0.3569655 -2.946897 3.209802e-03 0.0394160686
## Bace1    1377.1077      -1.037258 0.3245718 -3.195774 1.394565e-03 0.0231962646
## Ace      3182.8865      -1.036258 0.3587287 -2.888695 3.868442e-03 0.0432707008

4.2.4 Hippocampus, nSD, 18m vs 4m

##           baseMean log2FoldChange     lfcSE      stat       pvalue         padj
## Mapk1    1669.5639      -2.115931 0.7236660 -2.923905 3.456704e-03 0.0711093330
## Dlk1     1041.1257       2.071091 0.6164024  3.359966 7.795217e-04 0.0224502236
## Col6a1  19031.1594       1.760535 0.5218296  3.373774 7.414516e-04 0.0224502236
## Folr1    1832.4643      -1.709645 0.7620983 -2.243339 2.487498e-02 0.1733224198
## Th        538.3247       1.609919 0.3157554  5.098626 3.421274e-07 0.0001186777
## Synpr     318.4506      -1.486967 0.5361688 -2.773320 5.548758e-03           NA
## Synpo2   2752.3557       1.475591 0.6481139  2.276746 2.280137e-02 0.1716919266
## Htr2c    1130.0513      -1.473991 0.5587192 -2.638162 8.335682e-03 0.0999448930
## Crebbp    912.6200      -1.379936 0.5838201 -2.363632 1.809677e-02 0.1563561073
## Six3     3526.4818       1.367953 0.6393661  2.139546 3.239151e-02 0.1967242669
## Penk    18379.6041       1.359137 0.5305433  2.561783 1.041364e-02 0.1071117644
## Rims1    2200.4093      -1.342497 0.4946906 -2.713811 6.651411e-03 0.0957803213
## Dcn       844.5796      -1.286658 0.2845329 -4.522000 6.125812e-06 0.0005292701
## Dclk3   17352.4896       1.285261 0.4294304  2.992944 2.763009e-03 0.0596809860
## Gpr37    3190.4456      -1.283460 0.2562720 -5.008193 5.494339e-07 0.0001186777
## Acta2    1841.9538      -1.281820 0.4017026 -3.190969 1.417967e-03 0.0334730292
## Ddit4l    262.8605      -1.259404 0.4957763 -2.540267 1.107679e-02           NA
## Nectin3   798.3678      -1.248818 0.5164259 -2.418195 1.559773e-02 0.1405763749
## Cldn11  21811.2036      -1.245550 0.2561561 -4.862464 1.159336e-06 0.0001334128
## Adora2a  6936.5057       1.244071 0.6279937  1.981025 4.758851e-02 0.2355246313
## Igf2     7577.2872      -1.237929 0.6089652 -2.032841 4.206862e-02 0.2226103804
## Pdyn     2404.9656       1.224516 0.4406717  2.778749 5.456867e-03 0.0900876939
## Nrn1     3108.9032      -1.189883 0.4481541 -2.655075 7.929066e-03 0.0990135707
## Opalin   2716.5036      -1.166851 0.3018913 -3.865135 1.110277e-04 0.0059954941
## Tacr3     382.8694      -1.122741 0.5412695 -2.074274 3.805388e-02           NA
## Col11a1  2472.6758      -1.119806 0.4266917 -2.624392 8.680380e-03 0.0999448930
## Mog      8346.7775      -1.110528 0.2751478 -4.036112 5.434417e-05 0.0034383397
## Enpp2   20320.3993      -1.080720 0.4717670 -2.290792 2.197547e-02 0.1716919266
## Adarb2    729.0932      -1.039995 0.4698901 -2.213272 2.687887e-02 0.1786411276
## Fibcd1   4600.2944      -1.033393 0.2740133 -3.771324 1.623838e-04 0.0070149784
## Ccn2     1020.3759      -1.027369 0.3875189 -2.651145 8.021933e-03 0.0990135707
## Dlx2     1783.1703       1.023830 0.4607517  2.222085 2.627754e-02 0.1773733750
## Grin3a   1973.2670      -1.009012 0.4726768 -2.134677 3.278738e-02 0.1967242669
## Cd9      2190.5569      -1.000183 0.4423899 -2.260863 2.376773e-02 0.1716919266

4.3 Front Cortex Region

4.3.1 Front Cortex, 4m, SD vs nSD

##         baseMean log2FoldChange     lfcSE     stat     pvalue      padj
## Synpo2  5253.975       1.294972 0.5329267 2.429926 0.01510193 0.9945726
## Tcf7l2 10334.890       1.267829 0.5921721 2.140981 0.03227555 0.9945726
## Clic6   3319.993       1.066931 0.5031460 2.120520 0.03396220 0.9945726

4.3.2 Front Cortex, 4m, SD vs nSD

##        baseMean log2FoldChange     lfcSE     stat       pvalue      padj
## Dlk1   3535.329       2.697496 1.3066625 2.064417 0.0389782411 0.9976486
## Ngb    2151.579       1.313891 0.6156327 2.134212 0.0328254208 0.9976486
## Calb2 10668.088       1.119273 0.3264835 3.428267 0.0006074466 0.1512542
## Ntng1  5548.844       1.045397 0.4528420 2.308525 0.0209699630 0.9976486

4.3.3 Front Cortex, SD, 18m vs 4m

##           baseMean log2FoldChange     lfcSE      stat       pvalue        padj
## Mapk1    6255.2112      -2.513942 0.6472833 -3.883836 1.028214e-04 0.007659816
## Tnik     3185.3111      -1.665473 0.5598671 -2.974764 2.932142e-03 0.099762892
## Rims1    9884.3332      -1.653063 0.3675999 -4.496908 6.894888e-06 0.003447444
## Pten     3267.0055      -1.511649 0.5333828 -2.834078 4.595807e-03 0.135170786
## Crebbp   3116.4107      -1.473675 0.5455952 -2.701041 6.912289e-03 0.168269073
## Synpr     961.8203      -1.423123 0.4312627 -3.299899 9.671961e-04 0.048359807
## Npy1r    3110.9271      -1.415869 0.3545175 -3.993790 6.502543e-05 0.007659816
## Mas1     5805.0479      -1.355472 0.3499252 -3.873604 1.072374e-04 0.007659816
## Nrn1     8807.3603      -1.330843 0.3182181 -4.182174 2.887349e-05 0.007218373
## Kcnh7    5856.3683      -1.316154 0.4287390 -3.069826 2.141835e-03 0.089243134
## Htr2c    2574.0793      -1.309623 0.6199822 -2.112355 3.465599e-02 0.320275211
## Coch     3242.5834      -1.308947 0.3592633 -3.643420 2.690397e-04 0.016814980
## Aph1b    1362.3544      -1.288393 0.4878720 -2.640842 8.270020e-03 0.179783041
## Cd63     1858.8846      -1.229036 0.4046110 -3.037575 2.384899e-03 0.091726896
## Scimp    3214.2971      -1.178549 0.2970154 -3.967971 7.248715e-05 0.007659816
## Cdh9     2399.4879      -1.174131 0.3803598 -3.086895 2.022593e-03 0.089243134
## Cd2ap    5102.4494      -1.097587 0.4742872 -2.314182 2.065777e-02 0.264437984
## Synpo2   8661.0593       1.092095 0.5254055  2.078575 3.765646e-02 0.335192074
## Enpp2   49518.0321      -1.082679 0.4130321 -2.621295 8.759638e-03 0.182492463
## Nectin3  2785.1227      -1.081607 0.4692021 -2.305206 2.115504e-02 0.264437984
## Gpr63    3002.4449      -1.059907 0.3838702 -2.761108 5.760566e-03 0.151593838
## Gm14964  2786.5810      -1.015902 0.4583859 -2.216258 2.667384e-02 0.288920200

4.3.4 Front Cortex, nSD, 18m vs 4m

##           baseMean log2FoldChange     lfcSE      stat       pvalue        padj
## Mapk1    3104.2402      -2.218915 0.5739169 -3.866264 1.105152e-04 0.013703883
## Tnik     1768.3125      -1.581507 0.5027979 -3.145413 1.658523e-03 0.061697060
## Rims1    6144.3140      -1.542799 0.3896719 -3.959225 7.519345e-05 0.013703883
## Crebbp   1779.6250      -1.529439 0.5165919 -2.960633 3.070074e-03 0.091815104
## Ddit4l    499.3928      -1.444243 0.4328069 -3.336923 8.471145e-04          NA
## Kcnh7    4004.9201      -1.272078 0.4412429 -2.882942 3.939801e-03 0.099172287
## Nectin3  1595.6233      -1.260374 0.4410248 -2.857831 4.265475e-03 0.099172287
## Nrn1     6211.3790      -1.232641 0.3700891 -3.330661 8.664010e-04 0.046043025
## Coch     1950.6947      -1.209003 0.3287500 -3.677575 2.354615e-04 0.021897923
## Npy1r    1832.5588      -1.207238 0.3483518 -3.465572 5.291049e-04 0.035665480
## Igf2     6235.0451      -1.179828 0.4825696 -2.444887 1.448977e-02 0.215607760
## Ngb      1200.2031       1.151301 0.5441568  2.115752 3.436591e-02          NA
## Enpp2   22600.8521      -1.148215 0.2619749 -4.382920 1.170991e-05 0.004356085
## Slc6a3   1125.7597       1.130957 0.5427395  2.083794 3.717890e-02          NA
## Neurod6  5231.8513      -1.079257 0.4712125 -2.290384 2.199909e-02 0.282195202
## Calb2    6249.1469       1.054973 0.5081247  2.076209 3.787461e-02 0.352233887
## Mas1     4070.1741      -1.046227 0.3550125 -2.947013 3.208592e-03 0.091815104

4.4 CA1 Glut

4.4.1 CA1, 4m, SD vs nSD

##      baseMean log2FoldChange     lfcSE      stat     pvalue      padj
## Fosb 65.82303        -1.2315 0.5028387 -2.449096 0.01432151 0.9998024

4.4.2 CA1, 4m, SD vs nSD

##        baseMean log2FoldChange     lfcSE      stat     pvalue      padj
## Col6a1 46.47429      -1.099649 0.5210937 -2.110271 0.03483498 0.9981926

4.4.3 CA1, SD, 18m vs 4m

##            baseMean log2FoldChange     lfcSE      stat       pvalue
## Mapk1     152.56820      -3.060532 0.8974183 -3.410375 6.487372e-04
## Col6a1     75.84606       2.331295 0.5224536  4.462205 8.112053e-06
## Pten       44.49544      -1.832961 0.5045958 -3.632532 2.806535e-04
## Crebbp     61.76913      -1.659432 0.4804898 -3.453626 5.531029e-04
## Cd63       31.43783      -1.621291 0.5096757 -3.181025 1.467550e-03
## Rims1     112.71841      -1.610565 0.3295337 -4.887405 1.021736e-06
## Osr1       13.93035      -1.588537 0.6698127 -2.371614 1.771057e-02
## Scimp      68.04926      -1.570067 0.3590316 -4.373060 1.225171e-05
## Kcnh7     211.84604      -1.563109 0.4151966 -3.764743 1.667205e-04
## Aph1b      35.00426      -1.522892 0.5647031 -2.696801 7.000920e-03
## Gng2      147.05643      -1.452707 0.3047149 -4.767429 1.865913e-06
## Htr2c      12.58341      -1.410289 0.7140349 -1.975098 4.825706e-02
## Nrn1      247.86821      -1.393467 0.2670708 -5.217596 1.812600e-07
## Gabra1    447.43112      -1.382199 0.2992479 -4.618910 3.857613e-06
## Tgfbr1     12.03155      -1.363714 0.6638327 -2.054303 3.994634e-02
## Rgs5       20.29598      -1.345665 0.5288117 -2.544696 1.093730e-02
## Vip        22.45325      -1.313567 0.5571455 -2.357673 1.838986e-02
## Pthlh      92.33236       1.312689 0.4232590  3.101384 1.926185e-03
## Fam107a   202.83942      -1.278128 0.3466581 -3.687000 2.269134e-04
## Creb1      22.94129      -1.253724 0.5297952 -2.366432 1.796047e-02
## Mfsd2a     18.99395      -1.193663 0.5392621 -2.213513 2.686232e-02
## Cxcl10     28.87740       1.151695 0.4920407  2.340650 1.925021e-02
## Gpr63     239.21112      -1.132138 0.3694192 -3.064642 2.179305e-03
## Cd2ap      69.48275      -1.116352 0.4533377 -2.462518 1.379653e-02
## Fermt2    152.21579      -1.114068 0.3121525 -3.568985 3.583672e-04
## Rims2     213.95151      -1.100345 0.2967790 -3.707625 2.092119e-04
## Cd83       54.95034      -1.089725 0.4011008 -2.716836 6.590923e-03
## Enpp2     127.36040      -1.077678 0.3949238 -2.728825 6.356035e-03
## Cdh12      95.21613      -1.064576 0.3402567 -3.128745 1.755547e-03
## Gsto1      39.85407      -1.052179 0.4204573 -2.502464 1.233322e-02
## Lpl        29.81177      -1.046018 0.5176534 -2.020692 4.331162e-02
## Plp1      337.45238      -1.041314 0.2846385 -3.658374 2.538207e-04
## Serpina3n 157.09700      -1.014301 0.3173061 -3.196600 1.390575e-03
## Grm3       70.92527      -1.000590 0.3382539 -2.958103 3.095391e-03
##                   padj
## Mapk1     1.640378e-02
## Col6a1    5.743333e-04
## Pten      9.031941e-03
## Crebbp    1.506142e-02
## Cd63      2.980946e-02
## Rims1     1.808473e-04
## Osr1                NA
## Scimp     7.228506e-04
## Kcnh7     8.431293e-03
## Aph1b     6.044696e-02
## Gng2      2.201777e-04
## Htr2c               NA
## Nrn1      6.416603e-05
## Gabra1    3.413988e-04
## Tgfbr1              NA
## Rgs5                NA
## Vip                 NA
## Pthlh     3.099407e-02
## Fam107a   8.925259e-03
## Creb1               NA
## Mfsd2a              NA
## Cxcl10    1.329627e-01
## Gpr63     3.354234e-02
## Cd2ap     1.061733e-01
## Fermt2    1.057183e-02
## Rims2     8.925259e-03
## Cd83      5.832967e-02
## Enpp2     5.832967e-02
## Cdh12     3.011877e-02
## Gsto1     9.922635e-02
## Lpl       2.071934e-01
## Plp1      8.985254e-03
## Serpina3n 2.980946e-02
## Grm3      4.058523e-02

4.4.4 CA1, nSD, 18m vs 4m

##          baseMean log2FoldChange     lfcSE      stat       pvalue      padj
## Chrna6   19.67951       1.666178 0.4754129  3.504696 0.0004571284 0.2281071
## Nectin3  47.46258      -1.631437 0.5395209 -3.023863 0.0024956960 0.4151174
## Crebbp   55.58805      -1.392473 0.6546302 -2.127113 0.0334106741 0.9511837
## Rims1    96.25567      -1.178207 0.4683167 -2.515833 0.0118751318 0.8386956
## Fosb     80.55486       1.171907 0.5678902  2.063616 0.0390541737 0.9511837
## Col11a1 547.60932      -1.154765 0.3790488 -3.046482 0.0023153623 0.4151174
## Tnik     74.09373      -1.048673 0.5044715 -2.078755 0.0376398811 0.9511837
## Trem2    49.35988      -1.011562 0.4370855 -2.314335 0.0206493564 0.9511837

4.5 CA3 Glut

4.5.1 CA3, 4m, SD vs nSD

##       baseMean log2FoldChange     lfcSE     stat       pvalue        padj
## Calb2 29.82477       2.051544 0.4488261 4.570910 4.856107e-06 0.002428053
## Pomc  20.86806       1.612490 0.7007676 2.301034 2.138974e-02 0.999424500
## Lef1  21.37378       1.102830 0.5148673 2.141970 3.219591e-02 0.999424500

4.5.2 CA3, 4m, SD vs nSD

##     baseMean log2FoldChange   lfcSE      stat     pvalue     padj
## Agt 19.29474      -1.261918 0.54177 -2.329251 0.01984578 0.997665

4.5.3 CA3, SD, 18m vs 4m

##            baseMean log2FoldChange     lfcSE      stat       pvalue
## Mapk1      96.70723      -2.797088 0.9422508 -2.968518 2.992397e-03
## Nectin3    94.11829      -2.650630 0.9847415 -2.691701 7.108864e-03
## Fmo1       22.72425      -1.864992 0.7204081 -2.588799 9.631126e-03
## Rims1     125.30259      -1.804023 0.3509276 -5.140727 2.736775e-07
## Cdh9       80.74375      -1.710960 0.4120177 -4.152637 3.286652e-05
## Gpr63      54.51819      -1.681459 0.4957066 -3.392044 6.937330e-04
## Aph1b      12.14087      -1.608115 0.7086056 -2.269407 2.324357e-02
## Drd2       27.50701      -1.608077 0.5128373 -3.135647 1.714753e-03
## Sla        16.21457      -1.600248 0.7097770 -2.254578 2.415983e-02
## Nrn1      293.31061      -1.513779 0.3108338 -4.870058 1.115657e-06
## Cxcl10     17.83327       1.336723 0.5609055  2.383151 1.716515e-02
## Crebbp     38.56529      -1.304990 0.6297910 -2.072100 3.825613e-02
## Calb2      39.02454       1.284262 0.4614994  2.782804 5.389134e-03
## Cd2ap      45.94890      -1.275721 0.4892195 -2.607667 9.116165e-03
## Pten       32.75776      -1.267329 0.5498387 -2.304910 2.117159e-02
## Cdh12      45.33086      -1.250016 0.4222776 -2.960176 3.074635e-03
## Gsto1      24.06958      -1.222902 0.4947700 -2.471658 1.344883e-02
## Tlr4       24.76203      -1.212746 0.5234835 -2.316683 2.052099e-02
## Tnik       43.38206      -1.206358 0.4799521 -2.513496 1.195410e-02
## Klk6       27.27520       1.136663 0.4751948  2.391994 1.675711e-02
## Gng2      103.11553      -1.102622 0.3869352 -2.849630 4.377005e-03
## Neurod6   292.42755      -1.077181 0.3811013 -2.826496 4.706040e-03
## Serpina3n  70.41562      -1.074227 0.3552259 -3.024066 2.494016e-03
## Scimp      38.01897      -1.072117 0.4720622 -2.271136 2.313874e-02
## Cldn5     130.71945       1.055569 0.4638584  2.275628 2.286828e-02
## Fermt2     91.57595      -1.030736 0.3421934 -3.012146 2.594079e-03
## Bace1      49.40905      -1.007580 0.3874615 -2.600466 9.309731e-03
##                   padj
## Mapk1     0.0784031910
## Nectin3   0.0939642951
## Fmo1      0.0991256923
## Rims1     0.0000837453
## Cdh9      0.0033523850
## Gpr63     0.0424564579
## Aph1b               NA
## Drd2      0.0720600640
## Sla                 NA
## Nrn1      0.0001706954
## Cxcl10              NA
## Crebbp    0.2053750320
## Calb2     0.0884158530
## Cd2ap     0.0991256923
## Pten      0.1439668309
## Cdh12     0.0784031910
## Gsto1     0.1228233021
## Tlr4      0.1439668309
## Tnik      0.1179985350
## Klk6      0.1349388655
## Gng2      0.0884158530
## Neurod6   0.0884158530
## Serpina3n 0.0784031910
## Scimp     0.1475094521
## Cldn5     0.1475094521
## Fermt2    0.0784031910
## Bace1     0.0991256923

4.5.4 CA3, nSD, 18m vs 4m

##          baseMean log2FoldChange     lfcSE      stat       pvalue       padj
## Rims1   122.02774      -1.759470 0.4511505 -3.899963 0.0000962075 0.04810375
## Crebbp   32.82484      -1.717662 0.5431351 -3.162494 0.0015642387 0.26070645
## Rspo1    12.52315      -1.513906 0.6752653 -2.241943 0.0249650722 0.86205315
## Col6a1   74.09823       1.377491 0.4636508  2.970965 0.0029686518 0.37108148
## Synpr    17.53155      -1.253856 0.5627003 -2.228284 0.0258615946 0.86205315
## Tnik     49.15606      -1.228526 0.5329225 -2.305262 0.0211518791 0.86205315
## Htr1a    29.52066      -1.138947 0.4513009 -2.523699 0.0116127426 0.82948161
## Hsd11b1  20.24491      -1.112675 0.5402333 -2.059620 0.0394348615 0.93131111
## Gpr37    37.90748      -1.046958 0.4130462 -2.534725 0.0112535789 0.82948161
## Rims2   134.37693      -1.023151 0.3117266 -3.282205 0.0010299856 0.25749640

4.6 DG Glut

4.6.1 DG, 4m, SD vs nSD

##        baseMean log2FoldChange     lfcSE      stat     pvalue      padj
## Cd4    1.441795       4.001266 1.9877728  2.012940 0.04412099 0.9997526
## Cux2   1.615010      -3.987675 1.8577386 -2.146521 0.03183143 0.9997526
## Nnat   6.838911      -1.729596 0.8614498 -2.007773 0.04466741 0.9997526
## Nr4a1 12.890494      -1.368803 0.6770528 -2.021708 0.04320652 0.9997526
## Egr1  27.310567      -1.153685 0.5041164 -2.288528 0.02210677 0.9997526

4.6.2 DG, 4m, SD vs nSD

## [1] baseMean       log2FoldChange lfcSE          stat           pvalue        
## [6] padj          
## <0 rows> (or 0-length row.names)

4.6.3 DG, SD, 18m vs 4m

##           baseMean log2FoldChange     lfcSE      stat       pvalue         padj
## Creb1     8.838619      -3.540733 1.4029857 -2.523713 1.161227e-02           NA
## Osr1      4.312403      -3.531686 1.6380477 -2.156033 3.108106e-02           NA
## Mapk1   110.720229      -3.151802 1.1344168 -2.778345 5.463653e-03 0.0761206451
## Sulf2     6.545435      -2.934066 1.4668794 -2.000209 4.547769e-02           NA
## Pcdh11x  10.087379      -2.799634 1.2592253 -2.223299 2.619567e-02           NA
## Pten     27.204742      -2.280146 0.7753240 -2.940895 3.272656e-03 0.0617635780
## Igfbp6   13.685701      -2.166661 1.0276651 -2.108334 3.500212e-02           NA
## Batf3    13.905444      -2.061392 0.9783259 -2.107061 3.511229e-02           NA
## Drd2     15.229984      -1.978422 0.9188411 -2.153171 3.130526e-02           NA
## Npy1r    89.088059      -1.927346 0.4749452 -4.058040 4.948637e-05 0.0026833698
## Trib2    23.553423      -1.901210 0.7251365 -2.621866 8.744991e-03 0.0870524059
## Mfsd2a   23.696306      -1.843867 0.7014478 -2.628659 8.572227e-03 0.0870524059
## Rims1    87.128681      -1.674065 0.4453630 -3.758878 1.706769e-04 0.0053397478
## Crebbp   34.223984      -1.649559 0.6771776 -2.435933 1.485344e-02 0.1121690729
## Cp       21.131692      -1.642743 0.7288942 -2.253746 2.421214e-02           NA
## Nnat     23.658280      -1.588440 0.6832939 -2.324680 2.008906e-02 0.1293971759
## Adarb2   54.166987      -1.536173 0.5808529 -2.644686 8.176684e-03 0.0870524059
## Dkk3    120.215937       1.519698 0.3053695  4.976587 6.471515e-07 0.0001417262
## Nrn1    275.875815      -1.448143 0.3195334 -4.532055 5.841266e-06 0.0006396187
## Gabra1  140.589194      -1.442634 0.3599486 -4.007888 6.126415e-05 0.0026833698
## Cdh12    49.337250      -1.342794 0.4856149 -2.765142 5.689808e-03 0.0761206451
## Hs3st1   32.842991      -1.281491 0.5745614 -2.230382 2.572211e-02 0.1482406001
## Kctd4   229.707578      -1.247941 0.2864377 -4.356763 1.319999e-05 0.0009635994
## Bace1    49.699778      -1.239075 0.4955976 -2.500163 1.241361e-02 0.0970921578
## Gng2    114.342153      -1.208708 0.4193616 -2.882259 3.948357e-03 0.0617635780
## Ccl6     36.457623       1.102447 0.4892745  2.253229 2.424472e-02 0.1435025600
## Fermt2   78.033576      -1.099614 0.4320875 -2.544888 1.093129e-02 0.0970921578
## Rims2    81.157211      -1.028183 0.4096605 -2.509841 1.207855e-02 0.0970921578
## Prox1   308.020078      -1.002059 0.2626136 -3.815716 1.357886e-04 0.0049562837

4.6.4 DG, nSD, 18m vs 4m

##        baseMean log2FoldChange     lfcSE      stat       pvalue      padj
## Mapk1  61.53882      -2.648736 1.1590254 -2.285313 0.0222944657 0.9987521
## Rims1  63.32509      -1.563496 0.4604135 -3.395851 0.0006841558 0.3420779
## Adarb2 28.93418      -1.346367 0.6409590 -2.100551 0.0356804424 0.9987521
## Gng2   75.69529      -1.217834 0.4313223 -2.823489 0.0047503990 0.7103968
## Dkk3   81.20299       1.104258 0.3483491  3.169974 0.0015245266 0.3811316
## Nos1   40.84720      -1.086536 0.4572932 -2.376015 0.0175007333 0.9722630

4.7 Microglia

4.7.1 Microglia, 4m, SD vs nSD

##        baseMean log2FoldChange     lfcSE      stat     pvalue      padj
## Pilra  8.356982      -1.484263 0.7027468 -2.112088 0.03467892 0.9991502
## Nts    9.439281      -1.393225 0.6952182 -2.004011 0.04506883 0.9991502
## Kcnq1 27.739852      -1.285856 0.6186094 -2.078624 0.03765196 0.9991502

4.7.2 Microglia, 4m, SD vs nSD

##         baseMean log2FoldChange     lfcSE      stat     pvalue      padj
## Cxcl10  14.04880      -1.450298 0.7294729 -1.988145 0.04679569 0.9989715
## Ccdc153 19.29723      -1.210721 0.6141815 -1.971275 0.04869244 0.9989715

4.7.3 Microglia, SD, 18m vs 4m

##           baseMean log2FoldChange     lfcSE      stat       pvalue         padj
## Cxcl10    34.43829       3.185087 1.2507666  2.546508 1.088068e-02 1.308472e-01
## Ube3a    183.87194       3.032369 0.4585702  6.612659 3.774779e-11 1.770371e-08
## Mapk1     97.52984      -2.024096 0.8614472 -2.349646 1.879129e-02 1.728062e-01
## Pten     100.80738      -1.860455 0.5094786 -3.651685 2.605254e-04 1.018220e-02
## Gpr17    161.77838      -1.761952 0.3951373 -4.459087 8.230934e-06 6.433847e-04
## Lgals3    45.38724       1.741305 0.3973101  4.382735 1.171987e-05 7.852310e-04
## Ly9      553.75907       1.595102 0.2655153  6.007569 1.883252e-09 4.416226e-07
## Bace1     25.07478      -1.531592 0.5023875 -3.048626 2.298905e-03 4.538742e-02
## Nrn1      58.03720      -1.511798 0.4188369 -3.609514 3.067708e-04 1.106735e-02
## Rims1    113.85149      -1.458970 0.3577024 -4.078725 4.528343e-05 2.123793e-03
## Krt73     92.35455       1.404952 0.2944249  4.771852 1.825392e-06 2.853696e-04
## C4b       97.98965       1.344343 0.3257714  4.126645 3.680944e-05 1.918181e-03
## Crebbp    49.34710      -1.287271 0.5759229 -2.235144 2.540789e-02 2.248359e-01
## Car4      47.20873      -1.250344 0.3784741 -3.303646 9.543617e-04 2.237978e-02
## Jam2     129.66134      -1.232333 0.3609923 -3.413739 6.407798e-04 1.760904e-02
## Cst7      36.36832       1.149199 0.4001300  2.872065 4.077996e-03 6.595104e-02
## Gfap     707.23835       1.063775 0.2455991  4.331347 1.481997e-05 8.688205e-04
## Csf1     407.35253       1.061309 0.2960703  3.584653 3.375266e-04 1.130714e-02
## Cx3cr1 14167.31892      -1.051905 0.2289954 -4.593565 4.357368e-06 5.109014e-04
## Tacr2     32.85523      -1.039224 0.4183249 -2.484250 1.298247e-02 1.449710e-01
## Gng2     270.75816      -1.025675 0.3080212 -3.329885 8.688199e-04 2.144613e-02
## P2ry12  3897.50513      -1.009820 0.3126185 -3.230200 1.237035e-03 2.762711e-02
## Prkce    177.03247      -1.008273 0.3844606 -2.622565 8.727052e-03 1.106213e-01
## Hs3st1   100.65168       1.000271 0.3632286  2.753833 5.890180e-03 8.632795e-02
## Chrna7    26.53656      -1.000061 0.5010288 -1.996014 4.593235e-02 3.205807e-01

4.7.4 Microglia, nSD, 18m vs 4m

##           baseMean log2FoldChange     lfcSE      stat       pvalue         padj
## Ube3a    181.80186       3.041205 0.8960115  3.394159 6.883975e-04 1.351433e-02
## Mapk1     98.01886      -2.237669 0.5837262 -3.833422 1.263730e-04 3.625933e-03
## Lgals3    46.94724       1.781549 0.3610819  4.933918 8.059622e-07 1.002080e-04
## Ly9      639.09507       1.706257 0.1836924  9.288664 1.562367e-20 5.827628e-18
## Hs3st1    99.30783       1.539458 0.3805613  4.045230 5.227173e-05 2.166373e-03
## Prkce    180.71848      -1.509355 0.4519899 -3.339354 8.397334e-04 1.430500e-02
## Pten      98.23140      -1.478363 0.4949702 -2.986771 2.819410e-03 2.921222e-02
## Crebbp    57.62455      -1.472084 0.5195135 -2.833582 4.602955e-03 4.187567e-02
## Trhr      20.56049       1.405772 0.7167553  1.961300 4.984403e-02           NA
## Clec7a    48.15243       1.402349 0.3606876  3.887990 1.010779e-04 3.141839e-03
## Cd74     270.68265       1.359913 0.2938595  4.627767 3.696300e-06 2.757439e-04
## Gfap     731.29154       1.338545 0.2611368  5.125839 2.962161e-07 5.524431e-05
## Cxcr4     16.19788       1.319395 0.5787165  2.279864 2.261578e-02           NA
## Krt73     94.17857       1.303918 0.3043821  4.283821 1.837106e-05 9.789152e-04
## Car4      40.78166      -1.226681 0.4072136 -3.012376 2.592113e-03 2.762452e-02
## Cd2ap    232.74810      -1.213374 0.4297161 -2.823664 4.747814e-03 4.216511e-02
## Rims1     94.71936      -1.206083 0.3639595 -3.313783 9.204293e-04 1.430500e-02
## Pkp2      24.85369       1.205030 0.4868917  2.474946 1.332564e-02           NA
## Itgal     49.52770       1.192854 0.3593647  3.319341 9.023010e-04 1.430500e-02
## Cst7      51.11475       1.175153 0.3527500  3.331404 8.640904e-04 1.430500e-02
## Jam2     141.84737      -1.149856 0.3664407 -3.137904 1.701606e-03 2.115663e-02
## Csf1     459.62288       1.128637 0.2757863  4.092432 4.268722e-05 1.990292e-03
## Pdlim5   106.46560      -1.127467 0.3854098 -2.925371 3.440457e-03 3.290488e-02
## P2ry12  3928.08674      -1.101162 0.3413644 -3.225767 1.256356e-03 1.673645e-02
## Apoe   10100.52400       1.099799 0.2420314  4.544033 5.518791e-06 3.430848e-04
## C3        59.54743       1.080231 0.4888754  2.209624 2.713126e-02 1.556917e-01
## Cx3cr1 14371.50486      -1.069597 0.2214226 -4.830568 1.361442e-06 1.269545e-04
## Ccl6      79.96391      -1.034753 0.4369001 -2.368398 1.786531e-02 1.170984e-01
## Grin3a    33.37285      -1.032305 0.4768214 -2.164973 3.038975e-02 1.691847e-01
## Casp8    545.41043      -1.003078 0.3182875 -3.151485 1.624424e-03 2.089345e-02

4.8 Astrocyte

4.8.1 Astrocyte, 4m, SD vs nSD

## [1] baseMean       log2FoldChange lfcSE          stat           pvalue        
## [6] padj          
## <0 rows> (or 0-length row.names)

4.8.2 Astrocyte, 4m, SD vs nSD

##        baseMean log2FoldChange     lfcSE     stat      pvalue      padj
## Cxcl10 177.1741      -1.892756 0.6142599 -3.08136 0.002060574 0.9995905

4.8.3 Astrocyte, SD, 18m vs 4m

##           baseMean log2FoldChange     lfcSE      stat       pvalue         padj
## Cxcl10   219.02254       2.523149 0.5368487  4.699926 2.602553e-06 5.868758e-04
## Mapk1    733.82523      -2.159191 0.8969952 -2.407138 1.607810e-02 1.154801e-01
## Tnik     390.52383      -1.871317 0.4757218 -3.933637 8.366996e-05 5.390736e-03
## Aph1b    252.89006      -1.833210 0.4605169 -3.980766 6.869365e-05 5.390736e-03
## Pten     454.36091      -1.658461 0.4715872 -3.516764 4.368418e-04 1.393180e-02
## Ddit4l   325.01639      -1.588108 0.4543943 -3.495000 4.740614e-04 1.393180e-02
## Scimp    360.85337      -1.545617 0.2942883 -5.252051 1.504147e-07 6.783701e-05
## Fmo1     865.95003      -1.531348 0.4306553 -3.555856 3.767504e-04 1.393180e-02
## Clic6   1573.12697       1.463319 0.3598292  4.066703 4.768294e-05 5.376252e-03
## Crebbp   479.33902      -1.338766 0.4579029 -2.923689 3.459098e-03 4.588392e-02
## Gm14964 2112.37766      -1.253496 0.3355748 -3.735369 1.874404e-04 1.056695e-02
## Htr2c    146.94141      -1.239408 0.4578314 -2.707128 6.786812e-03 6.935394e-02
## Rims1    598.49478      -1.194565 0.3021002 -3.954200 7.679123e-05 5.390736e-03
## Tshr     100.83117      -1.191223 0.4239309 -2.809946 4.954985e-03           NA
## Synpr     78.66474      -1.175632 0.5228535 -2.248493 2.454479e-02           NA
## Mhrt     192.35960      -1.162943 0.3941672 -2.950380 3.173838e-03 4.588392e-02
## Cd63     758.06994      -1.101061 0.4108220 -2.680140 7.359130e-03 6.935394e-02
## Npy2r    231.55009      -1.098837 0.3597531 -3.054419 2.254965e-03 4.078358e-02
## Ube3a    285.65333       1.074286 0.3083617  3.483851 4.942544e-04 1.393180e-02
## Cd2ap    960.31017      -1.061344 0.4242341 -2.501789 1.235677e-02 9.894220e-02
## Grin3a  1637.97798      -1.050680 0.3209665 -3.273489 1.062286e-03 2.395455e-02
## Atp13a5 2455.37536      -1.021468 0.2857244 -3.575012 3.502121e-04 1.393180e-02
## Gng2     448.01979      -1.020429 0.3314888 -3.078321 2.081705e-03 4.078358e-02
## Bace1    809.58118      -1.019204 0.2445438 -4.167778 3.075834e-05 4.624004e-03
## Jam2    2444.87768      -1.008393 0.3065624 -3.289356 1.004170e-03 2.395455e-02

4.8.4 Astrocyte, nSD, 18m vs 4m

##          baseMean log2FoldChange     lfcSE      stat       pvalue      padj
## Chrna6   19.67951       1.666178 0.4754129  3.504696 0.0004571284 0.2281071
## Nectin3  47.46258      -1.631437 0.5395209 -3.023863 0.0024956960 0.4151174
## Crebbp   55.58805      -1.392473 0.6546302 -2.127113 0.0334106741 0.9511837
## Rims1    96.25567      -1.178207 0.4683167 -2.515833 0.0118751318 0.8386956
## Fosb     80.55486       1.171907 0.5678902  2.063616 0.0390541737 0.9511837
## Col11a1 547.60932      -1.154765 0.3790488 -3.046482 0.0023153623 0.4151174
## Tnik     74.09373      -1.048673 0.5044715 -2.078755 0.0376398811 0.9511837
## Trem2    49.35988      -1.011562 0.4370855 -2.314335 0.0206493564 0.9511837

Abbreviation

Cell types & Regions

Astro, Astrocyte;

ABC, arachnoid barrier cells;

BAM, border-associated macrophages;

BLA, Basolateral amygdala;

CB, cerebellum;

CGE, caudal ganglionic eminence;

CHOR, choroid plexus;

CNU, cerebral nuclei;

CR, Cajal–Retzius;

CT, corticothalamic;

CTX, cerebral cortex;

CTXsp, cortical subplate;

DC, dendritic cells;

DCO, dorsal cochlear nucleus;

DG, dentate gyrus;

EA, extended amygdala;

Endo, endothelial cells;

ENT, Entorhinal area;

ENTl, Entorhinal area, lateral part;

Epen, ependymal;

EPI, epithalamus;

ET, extratelencephalic;

GC, granule cell;

HB, hindbrain;

HPF, hippocampal formation;

HY, hypothalamus;

HYa, anterior hypothalamic;

IMN, immature neurons;

IT, intratelencephalic;

L6b, layer 6b;

LGE, lateral ganglionic eminence;

LH, lateral habenula;

LSX, lateral septal complex;

MB, midbrain;

MGE, medial ganglionic eminence;

MH, medial habenula;

MM, medial mammillary nucleus;

MY, medulla;

NN, non-neuronal;

NP, near-projecting;

NT, non-telencephalon;

OB, olfactory bulb;

OEC, olfactory ensheathing cells;

OLF, olfactory areas;

Oligo, oligodendrocytes;

OPC, oligodendrocyte precursor cells;

P, pons;

PAL, pallidum;

Peri, pericytes;

PIR, piriform cortex;

SMC, smooth muscle cells;

STR, striatum;

TE, telencephalon;

TH, thalamus;

UBC, unipolar brush cells;

VLMC, vascular leptomeningeal cells.

Neurotransmitter types

Chol, cholinergic;

Dopa, dopaminergic;

GABA, GABAergic;

Glut, glutamatergic;

Glyc, glycinergic;

Hist, histaminergic;

Nora, noradrenergic;

Sero, serotonergic

ADP, anterodorsal preoptic nucleus

AHN, anterior hypothalamic nucleus

ARH, arcuate hypothalamic nucleus

CLI, central linear nucleus raphe

CUN, cuneiform nucleus

DMH, dorsomedial nucleus of the hypothalamus

DMX, dorsal motor nucleus of the vagus nerve

IF, interfascicular nucleus raphe

LHA, lateral hypothalamic area

MDRN, medullary reticular nucleus

MPN, medial preoptic nucleus

MPO, medial preoptic area

MV, medial vestibular nucleus

NTS, nucleus of the solitary tract

PAG, periaqueductal grey

PARN, parvicellular reticular nucleus

PB, parabrachial nucleus

PBG, parabigeminal nucleus

PGRN, paragigantocellular reticular nucleus

PGRNd, paragigantocellular reticular nucleus, dorsal part

PH, posterior hypothalamic nucleus

PMv, ventral premammillary nucleus

PPN, pedunculopontine nucleus

PVa, periventricular hypothalamic nucleus, anterior part

PVHd, paraventricular hypothalamic nucleus, descending division

PVi, periventricular hypothalamic nucleus, intermediate part

PVpo, periventricular hypothalamic nucleus, preoptic part

PVR, periventricular region

RAmb, midbrain raphe nuclei

RL, rostral linear nucleus raphe

SBPV, subparaventricular zone

SNc, substantia nigra, compact part

SPIV, spinal vestibular nucleus

TMv, tuberomammillary nucleus, ventral part

VII, facial motor nucleus

VMPO, ventromedial preoptic nucleus

VTA, ventral tegmental area

ZI, zona incerta.